There are many reasons to regret the death of Stephen Jay Gould; one of the weightiest is that he never had time to finish his last book at its proper length. Even close to death, he had twice the energy, range, and ambition of most writers; and the result is a last testament which is about twice as long as it should have been.

At 1,400 pages, and weighing rather more than twice as much as the laptop on which I'm writing this, The Structure of Evolutionary Theory is obviously a book that has too many words. But you have to dig into it to discover the real disadvantage, which is that most of the words have far too many syllables. This isn't because they are technical. Some of the passages here deal with issues of real technical complexity and philosophical difficulty, and those are admirably clear. It is in the more general sections that the Latinate orotundities settle in great snowdrifts around the argument, so that the struggling reader is overwhelmed by a warm longing to lie down and rest and never rise again.

Yet struggle through the snowdrifts, fortify yourself with brandy if you must, and you will be rewarded. For the grand design of the book is impressive, and its ambitions worthwhile and close to achievement. What Gould has set out to write is an account of the evolution of evolutionary theory; to look at all the really interesting questions that have arisen since the Origin of Species and to settle the question of how much of the modern science that bears his name Darwin would recognise today. So there are chapters on the early alternatives to Darwinism: sections on the emergence of modern (anti-Gouldian) orthodoxy within evolutionary theory; one book within a book on the limits of adaptation; and another on Gould's first large theory, punctuated equilibrium. It is all a vast apologia, without, of course, any hint of apology.

For the last 20 or 30 years, Gould has stood for "pluralism", which, to his opponents, means woolly-mindedness. In The Structure of Evolutionary Theory , he explains what he really means. There is no chance, in a review of this length, of covering all his subjects, but it is possible to give a flavour of his argument. For a start, and non-controversially, there is the idea that a great deal of the raw material of evolutionary change is supplied by accident. Natural selection can design the bat's system of echolocation, but it hasn't yet produced a device for warding off mass extinctions. There is no doubt that natural selection makes a great designer, but there is reasonable argument about how much of the world we see is the product of design. Gould has always argued that his ene mies, and most of his colleagues, see too much design and too many adaptations in the world, and coopted from architecture the term "spandrel" to describe an undesigned feature which is a necessary consequence of one that is designed, but is then used as a base for further design.

The dispute is perhaps one between historians and engineers: Gould is a paleontologist as well as a historian of ideas. In both contexts, he is interested in evolution as an account of what actually happened. His opponents, one of whom, John Maynard Smith, actually trained as an engineer, are much more interested in Darwinism as a timeless mechanism or set of mechanisms. Most of the biologists I know spent their childhoods building things - it hardly mattered what, so long as the bits fitted together in a satisfyingly logical way. One professor of biology, when asked to be more precise, replied "bombs, rockets, radios". But Gould spent his childhood reading books and dreaming of dinosaurs. No wonder he became the scientist for the rest of us.

Gould's essays from Natural History magazine - of which the handsomely produced I Have Landed is the 10th and final volume - are matchless examples of the strengths of a historical imagination roaming across a scientific subject. They are also better trimmed than the long book, with far less fat around the meat of the argument, partly because most of the serious arguments in his essays are ventriloquised through other people. Gould resembled Isaiah Berlin, in that he could most successfully expound his own ideas when they were presented as coming from others. The historical sections of The Structure of Evolutionary Theory are packed full of evolutionary theory presented in the clearest and most comprehensible way. The avowedly theoretical sections are much more tangly, though the ideas he is presenting are not in themselves more difficult.

Nonetheless, he did manage to knot together in the final sections several of his lifelong themes in a very comprehensible way, among them his objection to "gene-centric" ideas of evolution. To the engineering mind, the wonderful thing about genes, ever since their chemical nature was unravelled by Watson and Crick, is that this nature turned out to be digital. DNA, like light and matter, comes in chunks that are precise and measurable. Just as the physicists were getting all woolly and mystical, the biologists got themselves a really hard science.

The differences of style harden into greater substance when you ask what the entities are on which natural selection can operate. Are they genes, or bodies, or even whole species? For Darwin, working 50 years before the word "gene" was even coined, they were organisms - individual bodies. Individual giraffes had more descendants because they had longer necks. Once genetic inheritance was discovered, it seemed obvious that genes were the only thing that natural selection could act on.

But this, while fascinating, has to be partly wrong. The meanings of a gene are the things about it that make some versions better than others in the eyes of natural selection, and this meaning, these advantages, must almost always appear in bodies. These might not be the body that the gene itself is found in - the plant genes that control the colours of flowers, and make them attractive to bees, are really selected because of the way that bees' eyes work. That was the argument of Richard Dawkins's second, technical book, The Extended Phenotype.

This seems to prove that you can reduce almost everything about evolution to genes. However, as Gould points out, gene-centrism reached a kind of reductio ad absurdum with the the discovery of "selfish" or "junk" DNA. This is the name given to bits of chromosomes, possibly proper genes, which are copied by the exuberance of the cell's own copying mechanisms for no reason at all so far as the organism is concerned. These are genes which really are directly selected for their own physical qualities, not for their effects on the physical qualities of the cells that surround them. Their existence shows that normal DNA is selected in a more complicated way.

The point at issue is really a confusion between copying and winnowing: selection is a two-stage process, endlessly repeated. Things are copied, then their copies are winnowed to select ones with certain qualities, and the survivors are copied again. But in genetic systems, copying and winnowing are separate process (except in the specialised case of junk or selfish DNA): the things that are copied - the genes - are not the things that are winnowed - the bodies. Neither the copying nor the winnowing can sensibly be called "selection" on its own.

Nonetheless, it makes sense to ask what sorts of things are winnowed, and here Gould does go out on a limb. He argues that not merely individual bodies, but populations, whole species, and even clades - related groups of species - can compete with each other in a Darwinian sense, and so become the objects of selection.

This idea brings together two of his constant themes, for he argues that adaptation at one level of the hierarchy is what produces the spandrels at the next level that provide the raw material for further adaptation in their turn. That would explain, for example, how the duplication of genes when they are copied into junk DNA, which is a product of purely molecular selection, nonetheless supplies the raw material or spandrels for natural selection to work on the organism.

It is not at all clear how much this would revolutionise biology, nor how Gould might reconcile this kind of multi-level selectionism with his other belief that much evolutionary change is essentially random. It was a consistent complaint of Gould's opponents that he oversold his own ideas. But he did have an enormous amount to oversell, and it is saddening to reflect that he will never now write more, or less.